Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid invariant sites LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant

We look at the higher-order phylogeny of mammals, analyzing in detail the c omplete mtDNA sequences of more than 40 species. We test the support for se veral proposed superordinal relationships. To this end, we apply a number o f recently programmed methods and approaches, plus better-established metho ds. New pairwise tests show highly significant evidence that amino acid fre quencies are changing among nearly all the genomes studied when unvaried si tes are ignored. LogDet amino acid distances, with modifications to take in to account invariant sites, are combined with bootstrapping and the Neighbo r Joining algorithm to account for these violations of standard models. To weight the more slowly evolving sites, we exclude the more rapidly evolving sites from the data by using "site stripping". This leads to changing opti mal trees with nearly all methods. The bootstrap support for many hypothese s varies widely between methods, and few hypotheses can claim unanimous sup port from these data. Rather, we uncover good evidence that many of the ear lier branching patterns in the placental subtree could be incorrect, includ ing the placement of the root. The tRNA genes, for example, favor a spit be tween the group hedgehog, rodents, and primates versus all other sequenced placentals. Such a grouping is not ruled out by the amino acid sequence dat a. A grouping of all rodents plus rabbit, the old Glires hypothesis, is als o feasible with stripped amino acid data, and rodent monophyly is also comm on. The elephant sequence allows confident rejection of the older taxon Fen ungulata (Simpson, 1945). In its place, the new taxa Scrotifera and Fereuun gulata are defined. A new Likelihood ratio test is used to detect differenc es between the optimal tree for tRNA Versus that for amino acids. While not clearly significant as made, some results indicate the test is tending tow ards significance with more general models of evolution. Individual placeme nt tests suggest alternative positions for hedgehog and elephant. Congruenc e arguments to support elephant and armadillo together are striking, sugges ting a superordinal group composed of Xenarthra and African endemic mammals , which in turn may be near the root of the placental subtree. Thus, while casting doubt on some recent conclusions, the analyses are also unveiling s ome interesting new possibilities.